[R] mapply, coxph, and model formula

[Christos Hatzis]

Instead of mapply, use lapply (it is more appropriate in this case anyway as
you have only one list that you need to iterate over):

lapply(df.list, function(x) coxph(form, x))


-Christos 


> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Erik Iverson
> Sent: Thursday, November 08, 2007 4:43 PM
> To: 'r-help at stat.math.ethz.ch'
> Subject: [R] mapply, coxph, and model formula
> 
> Hello -
> 
> I am wanting to create some Cox PH models with coxph (in package
> survival) using different datasets.
> 
> The code below illustrates my current approach and problem 
> with completing this.
> 
> ### BEGIN R SAMPLE CODE ##############################
> library(survival)
> 
> #Define a function to make test data
> makeTestDF <- function(n) {
>    times  <- sample(1:200, n, replace = TRUE)
>    event  <- rbinom(n, 1, prob = .1)
>    trt    <- rep(c("A","B"), each = n/2)
>    testdf <- data.frame(times,event,trt) }
> 
> #Create two sets of test data of different sizes
> testdf1 <- makeTestDF(100)
> testdf2 <- makeTestDF(200)
> 
> #Define a formula and call coxph
> form <- Surv(times, event) ~ trt
> coxph(form, testdf1) #Works
> coxph(form, testdf2) #Works
> 
> #Create a list of the two data.frames
> df.list <- list(testdf1, testdf2)
> 
> #Try to use mapply
> mapply(coxph, form, df.list)
> 
> ### END R SAMPLE CODE ###############################
> 
> The mapply call generates the following message:
> 
> Error in terms.default(formula, special, data = data) :
> 	no terms component
> 
> It appears from debugging that the formula argument passed 
> into coxph is simply `~` in this case, with class "name" 
> instead of "formula".
> 
> Any ideas on how I can get this to work using this approach?
> 
> Best,
> Erik Iverson
> iverson at biostat.wisc.edu
> 
>  > sessionInfo()
> R version 2.5.1 (2007-06-27)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA
> TE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8
> ;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC
> _MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
>   [1] "grid"      "grDevices" "datasets"  "tcltk"     "splines" 
> "graphics"
>   [7] "utils"     "stats"     "methods"   "base"
> 
> other attached packages:
>          debug      mvbutils  SPLOTS_1.2-6       reshape SPLOTS_1.3-22
>        "1.1.0"       "1.1.1"       "1.2-6"       "0.8.0"      "1.3-22"
>          Hmisc         chron      survival
>        "3.4-2"      "2.3-13"        "2.32"
> 
> ______________________________________________
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> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
>